Framing an independent, integrated and evidence-based evaluation of the state of Australia's biophysical and human environments

© 2015, The Author(s). Published by Taylor & Francis. A new approach was developed for Australia's 2011 national State of the Environment (SoE) report to integrate the assessment of biophysical and human elements of the environment. A Common Assessment and Reporting Framework (CARF) guided design and implementation, responding to jurisdictional complexity, outstanding natural diversity and ecosystem values, high levels of cultural and heritage diversity, and a paucity of national-scale data. The CARF provided a transparent response to the need for an independent, robust and evidence-based national SoE report. We conclude that this framework will be effective for subsequent national SoE assessments and other integrated national-scale assessments in data-poor regions

Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages

<p>Abstract</p> <p>Background</p> <p>The liver X receptors (LXRs) are oxysterol sensing nuclear receptors with multiple effects on metabolism and immune cells. However, the complete genome-wide cistrome of LXR in cells of human origin has not yet been provided.</p> <p>Results</p> <p>We performed ChIP-seq in phorbol myristate acetate-differentiated THP-1 cells (macrophage-type) after stimulation with the potent synthetic LXR ligand T0901317 (T09). Microarray gene expression analysis was performed in the same cellular model. We identified 1357 genome-wide LXR locations (FDR < 1%), of which 526 were observed after T09 treatment. <it>De novo </it>analysis of LXR binding sequences identified a DR4-type element as the major motif. On mRNA level T09 up-regulated 1258 genes and repressed 455 genes. Our results show that LXR actions are focused on 112 genomic regions that contain up to 11 T09 target genes per region under the control of highly stringent LXR binding sites with individual constellations for each region. We could confirm that LXR controls lipid metabolism and transport and observed a strong association with apoptosis-related functions.</p> <p>Conclusions</p> <p>This first report on genome-wide binding of LXR in a human cell line provides new insights into the transcriptional network of LXR and its target genes with their link to physiological processes, such as apoptosis.</p> <p>The gene expression microarray and sequence data have been submitted collectively to the NCBI Gene Expression Omnibus <url>http://www.ncbi.nlm.nih.gov/geo</url> under accession number GSE28319.</p

Conformational Polymorphism of cRNA of T-Cell-Receptor Genes as a Clone-Specific Molecular Marker for Cutaneous Lymphoma

A novel molecular assay for the detection and characterization of monoclonal lymphoid populations in clinical specimens was developed. The assay is based on the principle that upon non-denaturing polyacrylamide gel electrophoresis RNA molecules separate into several metastable conformational forms. These conformational polymorphisms strictly depend on the nucleotide sequence of the individual molecule. Using DNA from formalin-fixed, paraffin-embedded tissue of patients with mycosis fungoides, highly variable junctional sequences of rearranged T-cell receptor gamma genes were amplified by polymerase chain reaction. Subsequently, the polymerase chain reactions products were transcribed into complementary RNA and analyzed by non-denaturing polyacrylamide gel electrophoresis. In clinical specimens with a monoclonal lymphoid population, a clone-specific pattern of bands was identified representing conformational polymorphisms of cRNA molecules of rearranged T-cell receptor gamma genes of the predominant lymphoid clone. Three biopsies from one patient taken from different sites of the body over 3 years yielded an identical pattern of bands. This methodology provides a novel and rapid tool for the molecular identification and characterization of clonal lymphoid populations in clinical specimens. It is likely to be of special value for studies on the clonal evolution of lymphoid disorders of the skin

7T MRI in natalizumab-associated PML and ongoing MS disease activity: a case study

OBJECTIVE: To assess the ability of ultra-high-field MRI to distinguish early progressive multifocal leukoencephalopathy (PML) from multiple sclerosis (MS) lesions in a rare case of simultaneous presentation of natalizumab-associated PML and ongoing MS activity. METHODS: Advanced neuroimaging including 1.5T, 3T, and 7T MRI with a spatial resolution of up to 0.08 mm(3) was performed. RESULTS: 7T MRI differentiated between PML-related and MS-related brain damage in vivo. Ring-enhancing MS plaques displayed a central vein, whereas confluent PML lesions were preceded by punctate or milky way-like T2 lesions. CONCLUSIONS: Given the importance of early diagnosis of treatment-associated PML, future systematic studies are warranted to assess the value of highly resolving MRI in differentiating between early PML- and MS-induced brain parenchymal lesions